Source code for allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata.multi_plane_metadata

from pynwb import NWBFile

from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.field_of_view_shape import FieldOfViewShape  # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.imaging_depth import ImagingDepth  # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata.imaging_plane_group import ImagingPlaneGroup  # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_container_id import OphysContainerId  # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_experiment_metadata import OphysExperimentMetadata  # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_session_id import OphysSessionId  # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_project_code import OphysProjectCode  # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.targeted_imaging_depth import TargetedImagingDepth  # NOQA
from allensdk.internal.api import PostgresQueryMixin


[docs]class MultiplaneMetadata(OphysExperimentMetadata):
    def __init__(self,
                 ophys_experiment_id: int,
                 ophys_session_id: OphysSessionId,
                 ophys_container_id: OphysContainerId,
                 field_of_view_shape: FieldOfViewShape,
                 imaging_depth: ImagingDepth,
                 targeted_imaging_depth: TargetedImagingDepth,
                 imaging_plane_group: ImagingPlaneGroup,
                 project_code: OphysProjectCode = OphysProjectCode()):
        super().__init__(
            ophys_experiment_id=ophys_experiment_id,
            ophys_session_id=ophys_session_id,
            ophys_container_id=ophys_container_id,
            field_of_view_shape=field_of_view_shape,
            imaging_depth=imaging_depth,
            targeted_imaging_depth=targeted_imaging_depth,
            project_code=project_code
        )
        self._imaging_plane_group = imaging_plane_group

[docs]    @classmethod
    def from_lims(
            cls, ophys_experiment_id: int,
            lims_db: PostgresQueryMixin) -> "MultiplaneMetadata":
        ophys_experiment_metadata = OphysExperimentMetadata.from_lims(
            ophys_experiment_id=ophys_experiment_id, lims_db=lims_db)
        imaging_plane_group = ImagingPlaneGroup.from_lims(
            ophys_experiment_id=ophys_experiment_id, lims_db=lims_db)
        return cls(
            ophys_experiment_id=ophys_experiment_metadata.ophys_experiment_id,
            ophys_session_id=ophys_experiment_metadata._ophys_session_id,
            ophys_container_id=ophys_experiment_metadata._ophys_container_id,
            field_of_view_shape=ophys_experiment_metadata._field_of_view_shape,
            imaging_depth=ophys_experiment_metadata._imaging_depth,
            targeted_imaging_depth=ophys_experiment_metadata._targeted_imaging_depth,  # noqa E501
            project_code=ophys_experiment_metadata._project_code,
            imaging_plane_group=imaging_plane_group
        )

[docs]    @classmethod
    def from_json(cls, dict_repr: dict) -> "MultiplaneMetadata":
        ophys_experiment_metadata = super().from_json(dict_repr=dict_repr)
        imaging_plane_group = ImagingPlaneGroup.from_json(dict_repr=dict_repr)
        return cls(
            ophys_experiment_id=ophys_experiment_metadata.ophys_experiment_id,
            ophys_session_id=ophys_experiment_metadata._ophys_session_id,
            ophys_container_id=ophys_experiment_metadata._ophys_container_id,
            field_of_view_shape=ophys_experiment_metadata._field_of_view_shape,
            imaging_depth=ophys_experiment_metadata._imaging_depth,
            targeted_imaging_depth=ophys_experiment_metadata._targeted_imaging_depth,  # noqa E501
            project_code=ophys_experiment_metadata._project_code,
            imaging_plane_group=imaging_plane_group
        )

[docs]    @classmethod
    def from_nwb(cls, nwbfile: NWBFile) -> "MultiplaneMetadata":
        ophys_experiment_metadata = super().from_nwb(nwbfile=nwbfile)
        imaging_plane_group = ImagingPlaneGroup.from_nwb(nwbfile=nwbfile)
        return cls(
            ophys_experiment_id=ophys_experiment_metadata.ophys_experiment_id,
            ophys_session_id=ophys_experiment_metadata._ophys_session_id,
            ophys_container_id=ophys_experiment_metadata._ophys_container_id,
            field_of_view_shape=ophys_experiment_metadata._field_of_view_shape,
            imaging_depth=ophys_experiment_metadata._imaging_depth,
            targeted_imaging_depth=ophys_experiment_metadata._targeted_imaging_depth,  # noqa E501
            project_code=ophys_experiment_metadata._project_code,
            imaging_plane_group=imaging_plane_group
        )

    @property
    def imaging_plane_group(self) -> int:
        return self._imaging_plane_group.plane_group

    @property
    def imaging_plane_group_count(self) -> int:
        # TODO this is at the wrong level of abstraction.
        #  It is an attribute of the session, not the experiment.
        #  Currently, an Ophys Session metadata abstraction doesn't exist
        return self._imaging_plane_group.plane_group_count
Source code for allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata.multi_plane_metadata

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